Volume 15, Issue 2, Pages 201-213 (February 2007) Crystal Structures of the p21-Activated Kinases PAK4, PAK5, and PAK6 Reveal Catalytic Domain Plasticity of Active Group II PAKs  Jeyanthy Eswaran, Wen Hwa Lee, Judit É. Debreczeni, Panagis Filippakopoulos, Andrew Turnbull, Oleg Fedorov, Sean W. Deacon, Jeffrey R. Peterson, Stefan Knapp  Structure  Volume 15, Issue 2, Pages 201-213 (February 2007) DOI: 10.1016/j.str.2007.01.001 Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 1 Overall Structures of Group II PAKs and Sequence Comparisons (A) Ribbon diagram showing a structural overview of PAK5. Secondary-structure elements were determined by using the program ICM Pro 3.4-8 (Molsoft LLC) and have been labeled according to a nomenclature established for PKA. The helices are shown in red, β strands are shown in green, and the 310 helices are shown in magenta. The phosphorylated serine in the activation segment is shown in ball and stick representation. (B) Superimposition of all catalytic domains on Cα positions of the C-terminal lobe. Apo-PAK4 is shown in green, PAK4Etgly is shown in magenta, the PAK4 purine complex is shown in yellow, PAK5 is shown in cyan, the PAK5 purine complex is shown in orange, and apo-PAK6 is shown in red. (C) Sequence alignment of PAK4, PAK5, PAK6, and PAK1. The blue asterisk marks the Arg487 (PAK5) conserved in group II PAKs. The red asterisk indicates residues involved in the αC activation loop anchor, and the cyan asterisk indicates the putative activation segment phosphoryation site of MKK6. The autophosphorylation site is indicated by “P.” Secondary-structure elements are colored and labeled as in (A). Structure 2007 15, 201-213DOI: (10.1016/j.str.2007.01.001) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 2 Structural Comparison of Activation Segments (A) Superimposition of the activation segments of group II PAKs showing conserved interactions: the PAK4 purine complex is shown in yellow, apo-PAK5 is shown in cyan, the PAK5 purine complex is shown in orange, and PAK6 is shown in red. The hydrogen bond network formed by the phosphoserine residue is shown, and interacting residues are labeled by using PAK5 numbering. (B) Superimposition comparing the activation segment of PAK1 (activated PAK1 mutant T423E, green) with group II PAKs (PAK5 purine complex, semitransparent); both proteins show similar activation segment conformation and interactions indicating that the glutamate residue successfully mimics the PAK1 phosphothreonine. Structure 2007 15, 201-213DOI: (10.1016/j.str.2007.01.001) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 3 Binding of the Purine Inhibitor (A and B) Superimposition of PAK4 and PAK5 showing the (A) binding modes of the purine inhibitor and (B) interaction with active site residues in PAK4. A superimposition of the C-terminal lobes was used to generate the figure shown in (A). PAK4 is shown in yellow, and PAK5 is shown in orange. Structure 2007 15, 201-213DOI: (10.1016/j.str.2007.01.001) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 4 PAK5 Domain Movements (A–C) Structural rearrangements observed upon binding of the inhibitor in PAK5 (apo, cyan; purine complex, orange). (A) Superimposition with the C-terminal lobe. Hinges defined by DymDom (Hayward and Lee, 2002) are highlighted in magenta. (B) Close-up of the hinge region, rotated 180° from the view shown in (A) with the PAK5 purine complex (orange). Conserved residues forming the salt bridge linking the N- and C-terminal lobes are shown. (C) Superimposition with the core β sheet of the N-terminal lobes of apo-PAK5 (cyan) and the PAK5 purine complex highlighting the decomposed movements of the glycine-rich loop (flapping) and the αC helix (swinging). Structure 2007 15, 201-213DOI: (10.1016/j.str.2007.01.001) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 5 Rearrangement of Helix αC (A) Superimposition of central residues in the PAK5 αC helices showing the remodeling of the αC termini. The central residues stay in position, whereas conversion into an active state (PAK5 purine complex) results in the addition of an N-terminal α helix and disruption of the αC terminus. (B) Structural changes at the αC C terminus brings Asn493 (Asn365, PAK4) into position to hydrogen bond with the DFG glycine (Gly588) and a conserved activation segment cysteine (Cys590 and Cys462 in PAK5 and PAK4, respectively), resulting in the formation of the αC anchor point with the activation segment. In the PAK4 structures, this movement is not completed, and only one hydrogen bond is formed with Cys462. (C) Swinging movement of the conserved αC Arg487 (Arg359 in PAK4) between the glycine-rich loop and the phosphoserine activation loop residue. Upon extension of the αC helix by one turn at the N –terminus, Arg487 forms three hydrogen bonds with the glycine-rich loop, stabilizing an extremely closed conformation (PAK5 purine complex, orange). In the short αC conformation, the corresponding arginine in PAK4 interacts with the phosphoserine residue in the activation segment. This conformation also results in a partially open conformation of the glycine-rich loop stabilized by a hydrogen bond formed by the conserved Gln357. When αC swings away (as observed in apo-PAK5, cyan, or PAK6 [not shown]), the N- and C-terminal anchor points break, resulting in an open glycine-rich loop conformation. During the swinging movement, Arg487 in the PAK5 apo structure was observed in a disordered state beyond the γ carbon (indicated by white balls and sticks). Structure 2007 15, 201-213DOI: (10.1016/j.str.2007.01.001) Copyright © 2007 Elsevier Ltd Terms and Conditions

Figure 6 Model Showing Conformational Changes in Group II PAKs (A and B) The N-terminal lobe is represented as red wire-frame (apo) and white surface (closed conformation). Secondary-structure elements involved in the domain movements are shown and colored in cyan (apo) and orange (closed conformation). Red sticks indicate positions of the three anchor points (see main text), and magenta CPK spheres depict the purine inhibitor. The clamping (movement 1) is shown in the (A) overview, while the detailed view in (B) depicts the closure of the cofactor binding site (movement 2) and the repositioning of αC (movement 3). Structure 2007 15, 201-213DOI: (10.1016/j.str.2007.01.001) Copyright © 2007 Elsevier Ltd Terms and Conditions